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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG

Basic information

species Vitis vinifera
transcript Vv14s0068g02040.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagata-ttattattattttgaattcttaatagttctataatttgtttctt--ttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
    ||||      ||    |||  |  ||       |   | ||| ||| |   ||  |||   ||   ||| | | |   |   ||   |     || |||||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||||||||| |||||||| ||||||
---ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
---aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
     ||| | ||  |  |    |    ||   |   |||   ||  |  | ||||   ||| || || |  ||  |   | |  || |    | | || |||||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||| ||||| |||||||| ||||||
attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagtt-gattatttgcttactttgaaagtc--ctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G25870.2 (Glycine max), 3'ss of exon 3
---aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG----------------
     ||| | ||  |  |    |    ||   |   |||   ||  |  | ||||   ||| || || |  ||  |   | |  || |    | | || |||||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||| ||||| |||||||| ||||||                
attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagtt-gattatttgcttactttgaaagtc--ctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAGGTAGTAGAATATAGGA

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 3
--aaaatcttaaggttttatacatttatggt--tagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
      |||   | |||| |    | ||     | ||||||   |||  |    ||| |   | |||||  |   |||  |||  | | |  || ||| |  ||||| | | |||||| ||  |||| |||||| | || || |||||||||||||| |||||||| || || |||||||| ||||||
gtttgttctcgtgctttttttttgtcataacaatggttttg---atgctaccatttactgaaaatttgatgttcgaattattccgtgaatgattccttgtttagGCAACAACTTTTGGAGGTACTAATATTGATGCTACTGCTTGGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S4_323V6.1 (Physcomitrella patens), 3'ss of exon 2
aaaatcttaaggttttatacatt-tatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
 ||     |     ||  || |  | ||    ||     |  | || ||  ||  |       |   |||| |    |  | |      | | | | ||||||||| |||||||| ||||||||||| ||||||||||| ||||||||||| |||||    || || || || |||||||| |||
caaggaggacctacttggacgtcctctgacctgtgggtggtgtcaaggac-ttgcttcagacgtaggttctcatgtatggtgtttacattctgtatgacagGCAGCAAGTTTTGGAGGCTCTAACATAGATCCAACCGCCTGGGAAGACAAGAAATGTCGGGGAGAGTCAAGATTTCCTGCCCAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
 |      ||| |    | ||      || || ||   | ||| |  ||||| ||  |  | |||  |  ||||     | |  |   | | | | ||||||||| |||||||| ||||| ||||| || |||||||| ||||||||||| |||||   ||| |||||||| ||||||||||||
-agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt-ctggtatgaggtgctaatg--catgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S168_104V6.1 (Physcomitrella patens), 3'ss of exon 3
---aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
   ||      ||| |    | ||      || || ||   | ||| |  ||||| ||  |  | |||  |  ||||     | |  |   | | | | ||||||||| |||||||| ||||| ||||| || |||||||| ||||||||||| |||||   ||| |||||||| ||||||||||||
gagaagcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt-ctggtatgaggtgctaatg--catgtcgtcattctttatgacagGCAGCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 2
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttc-ttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
                       ||  | ||  | | | |     |  | | |   | || ||||    |    ||| | |   ||||  |   | ||||||| || |||||||||||||| ||||| ||||| || || ||||||||||| || ||    || |||||  |||| ||||| |||
----------------------gtaaagctacctct-ctcgcaggatttgtgacactcatgttga----tggcgagtccaaacttttgcgtgactctacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG

upper sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ18285 (Selaginella moellendorffii), 3'ss of exon 2
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttc-ttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
                       ||  | ||  | | | |     |  | | | | | || ||||    |    | | | |   ||||  |   | ||||||| || |||||||||||||| ||||| ||||| || || ||||||||||| || ||    || |||||  |||| ||||| |||
----------------------gtaaagctacctct-ctctcaggatttgtgactctcatgttga----tggcgaatccaaacttttgcgtgactctacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|352795214|gb|FQ477324.1|FQ477324
EST:     CTTTGTTTCTCTATAACTACACTACTCACCCATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACAT
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACAT
EST: gi|110702016|gb|EE080244.1|EE080244
EST:     TTTGTTTCTCNTATA-CTACACTACTCACCAATTGCATGGTATTTTTGAA                         GCAGCTAGTTTTGGGGGCTCTTACATTGATCCA-CCGCATGGGAAGACAAA
genomic: TTTGTTTCTC-TATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110689556|gb|EE065885.1|EE065885
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAA                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110689555|gb|EE065884.1|EE065884
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAA                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAAC-GCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|30251482|gb|CB969215.1|CB969215
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|33405079|gb|CF210706.1|CF210706
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110396191|gb|EC961872.1|EC961872
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110709022|gb|EE084118.1|EE084118
EST:     -TTTGTTTCTCTATAACTACACTACTCACCAATTGCCTGGTATTTTTGAA                         GCAGCTAGTTTTGGG
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGG
EST: gi|351029823|gb|FQ427663.1|FQ427663
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110384179|gb|EC948598.1|EC948598
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110687785|gb|EE065593.1|EE065593
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAA                         GCAGCTAGTTTTGGGGGCTCTAACA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACA
EST: gi|110687073|gb|EE064163.1|EE064163
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110687425|gb|EE064823.1|EE064823
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|26257057|gb|CA808120.1|CA808120
EST:     TTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTTGAG                         GCAGCTAGTTTTGGGGGGCTCTAACATTGATCCAACCGCATG
genomic: TTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTT-GAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGG-CTCTAACATTGATCCAACCGCATG
EST: gi|351019333|gb|FQ429493.1|FQ429493
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAA
EST: gi|110688436|gb|EE066988.1|EE066988
EST:     CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAG                         GCAGCTAGTTTTGGGGGCTCTAA
genomic: CTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGAGgtttgtactt ... tcttttacagGCAGCTAGTTTTGGGGGCTCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
                      tcttaat  putative branch site (score: 3)
                                       tttgtttcttttac  putative PPT
     ttattattattttgaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - -tggttag
- - - - - - - - - - - - - - - - - - - gcatgaa